Variant report

Variant	rs2571996
Chromosome Location	chr7:99515100-99515101
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:99513401..99515939-chr7:99585193..99587203,2	K562	blood:
2	chr7:99514062..99516474-chr7:99604675..99606310,2	MCF-7	breast:
3	chr7:99497251..99500127-chr7:99514363..99515928,2	K562	blood:
4	chr7:99514836..99517773-chr7:99723238..99724823,2	K562	blood:
5	chr7:99513066..99515933-chr7:99589978..99591835,2	K562	blood:
6	chr7:99436167..99437949-chr7:99514061..99515612,2	MCF-7	breast:
7	chr7:99513908..99516258-chr7:99668490..99670311,2	K562	blood:

Variant related genes	Relation type
ENSG00000214309	Chromatin interaction
ENSG00000235713	Chromatin interaction
ENSG00000242798	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1025576	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1048705	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10808114	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1121592	0.97[ASN][1000 genomes]
rs13310903	0.82[ASN][1000 genomes]
rs1865472	0.97[ASN][1000 genomes]
rs2060452	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2082744	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2082745	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2247761	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2247762	0.96[ASN][1000 genomes]
rs2525542	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2527899	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527900	0.97[ASN][1000 genomes]
rs2527901	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527902	0.97[ASN][1000 genomes]
rs2527903	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2527904	0.97[ASN][1000 genomes]
rs2527906	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527908	0.97[ASN][1000 genomes]
rs2527909	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527911	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527912	0.96[ASN][1000 genomes]
rs2527913	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527914	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527915	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527916	0.97[ASN][1000 genomes]
rs2527918	0.96[ASN][1000 genomes]
rs2527919	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527920	0.96[ASN][1000 genomes]
rs2527921	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527922	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527925	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2527926	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2527927	0.91[ASN][1000 genomes]
rs2571991	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2571992	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571993	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571994	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571995	0.97[ASN][1000 genomes]
rs2571997	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571998	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571999	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2572000	0.96[ASN][1000 genomes]
rs2572002	0.91[ASN][1000 genomes]
rs2572003	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2572005	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2572006	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2572008	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2572009	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2572010	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2572011	0.94[ASN][1000 genomes]
rs2572012	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2572013	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2572015	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2572018	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2572019	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2572022	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2572024	0.80[AMR][1000 genomes]
rs4727439	0.96[ASN][1000 genomes]
rs474229	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs503115	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7781442	0.96[ASN][1000 genomes]
rs7809747	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2571996	TRIM4	cis	Esophagus Muscularis	GTEx
rs2571996	TRIM4	cis	Whole Blood	GTEx
rs2571996	TRIM4	cis	Thyroid	GTEx
rs2571996	TRIM4	cis	Stomach	GTEx
rs2571996	PILRB	Cis_1M	lymphoblastoid	RTeQTL
rs2571996	TRIM4	cis	Artery Tibial	GTEx
rs2571996	TRIM4	cis	Nerve Tibial	GTEx
rs2571996	TRIM4	cis	Adipose Subcutaneous	GTEx
rs2571996	TRIM4	cis	Esophagus Mucosa	GTEx
rs2571996	TRIM4	cis	lung	GTEx
rs2571996	TRIM4	cis	Artery Aorta	GTEx
rs2571996	TRIM4	cis	Skin Sun Exposed Lower leg	GTEx
rs2571996	TRIM4	Cis_1M	lymphoblastoid	RTeQTL
rs2571996	TRIM4	cis	Muscle Skeletal	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99492600-99516600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:99503000-99516400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr7:99506400-99515800	Weak transcription	Fetal Heart	heart
4	chr7:99507000-99515600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr7:99507200-99516000	Weak transcription	Esophagus	oesophagus
6	chr7:99507200-99516400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr7:99507200-99516400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr7:99507400-99515800	Weak transcription	Colonic Mucosa	Colon
9	chr7:99507800-99515600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr7:99511800-99515400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr7:99512800-99515200	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr7:99512800-99515200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr7:99512800-99515400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
14	chr7:99513000-99515200	Genic enhancers	Liver	Liver
15	chr7:99513200-99515200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr7:99513200-99515200	Genic enhancers	HepG2	liver
17	chr7:99513200-99515400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr7:99513200-99515600	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr7:99513200-99515800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr7:99513400-99515200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr7:99513400-99515200	Strong transcription	Aorta	Aorta
22	chr7:99513400-99515200	Genic enhancers	Stomach Smooth Muscle	stomach
23	chr7:99513400-99515400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr7:99513400-99515600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr7:99513400-99515800	Genic enhancers	Primary B cells from peripheral blood	blood
26	chr7:99513600-99515600	Genic enhancers	Primary T cells from cord blood	blood
27	chr7:99513800-99515200	Genic enhancers	Duodenum Mucosa	Duodenum
28	chr7:99513800-99515400	Genic enhancers	Colon Smooth Muscle	Colon
29	chr7:99513800-99515600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr7:99513800-99515600	Genic enhancers	Fetal Stomach	stomach
31	chr7:99514000-99515200	Genic enhancers	Fetal Brain Female	brain
32	chr7:99514000-99515400	Genic enhancers	Adipose Nuclei	Adipose
33	chr7:99514000-99515400	Genic enhancers	Brain Angular Gyrus	brain
34	chr7:99514000-99515400	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr7:99514000-99515400	Enhancers	Ovary	ovary
36	chr7:99514000-99515400	Genic enhancers	Thymus	Thymus
37	chr7:99514000-99515600	Genic enhancers	K562	blood
38	chr7:99514200-99515200	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr7:99514200-99515400	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr7:99514200-99515600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr7:99514200-99516200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr7:99514400-99515200	Genic enhancers	Brain Inferior Temporal Lobe	brain
43	chr7:99514400-99515200	Weak transcription	Small Intestine	intestine
44	chr7:99514400-99515400	Genic enhancers	Primary T cells fromperipheralblood	blood
45	chr7:99514400-99515400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr7:99514400-99515400	Enhancers	Brain Germinal Matrix	brain
47	chr7:99514400-99515400	Genic enhancers	Fetal Intestine Small	intestine
48	chr7:99514400-99515400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
49	chr7:99514400-99515400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
50	chr7:99514400-99515600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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